I don't see that happening, at least not in full. I can see Ynnead ascending, I can see Slaanesh being cast out.
But a traitor legion and primarch doing a full 180, and the Imperium being okay with this just doesn't sit right. Especially with it being Fulgrim, and especially with Guilleman being the one in charge. Maybe elements of the EC would be freed from Slaanesh' influence and try to rejoin the Imperium under penance, but even then I see it being a pretty spotty issue. More likely it would be similar to the AoS situation. Slaanesh is cast down, but its daemons and mortal followers keep fighting. Or perhaps Slaanesh will not be defeated this time around.
Not least of which because it would invalidate a lot of people's armies, and I don't see gw being that bold at this stage.
Nonsense is our Salvation